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Fix LSP warnings on pipeline template #3905

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Merged
mashehu merged 7 commits into from
Nov 18, 2025
+15 −14
Merged

Fix LSP warnings on pipeline template #3905

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d0a40db
Merge pull request #3833 from nf-core/dev
mirpedrol Oct 15, 2025
99b23f0
Merge pull request #3838 from nf-core/dev
mashehu Oct 16, 2025
5f02cfe
Fix LSP warnings
dialvarezs Nov 17, 2025
44d3c85
Merge branch 'dev' into fix-lsp-warnings
dialvarezs Nov 17, 2025
88745bc
Update changelog
dialvarezs Nov 17, 2025
9ee3891
Update subworflow checksum
dialvarezs Nov 17, 2025
c4161da
Merge branch 'dev' into fix-lsp-warnings
mashehu Nov 18, 2025
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,7 @@

- Change GitHub Codespaces badge style ([#3869](https://github.com/nf-core/tools/pull/3869) and [#3873](https://github.com/nf-core/tools/pull/3873))
- Update multiqc to 1.32 ([#3878](https://github.com/nf-core/tools/pull/3878))
- Fix LSP warnings in pipeline template ([#3905](https://github.com/nf-core/tools/pull/3905))

### Linting

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2 changes: 1 addition & 1 deletion nf_core/pipeline-template/modules.json
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Expand Up @@ -28,7 +28,7 @@
},
"utils_nfcore_pipeline": {
"branch": "master",
"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
"git_sha": "271e7fc14eb1320364416d996fb077421f3faed2",
"installed_by": ["subworkflows"]
}{% if nf_schema %},
"utils_nfschema_plugin": {
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6 changes: 3 additions & 3 deletions nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
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Expand Up @@ -43,7 +43,7 @@ workflow PIPELINE_INITIALISATION {

main:

ch_versions = Channel.empty()
ch_versions = channel.empty()

//
// Print version and exit if required and dump pipeline parameters to JSON file
Expand Down Expand Up @@ -72,7 +72,7 @@ workflow PIPELINE_INITIALISATION {
\033[0;35m {{ name }} ${workflow.manifest.version}\033[0m
-\033[2m----------------------------------------------------\033[0m-
"""
after_text = """${workflow.manifest.doi ? "\n* The pipeline\n" : ""}${workflow.manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${workflow.manifest.doi ? "\n" : ""}
after_text = """${workflow.manifest.doi ? "\n* The pipeline\n" : ""}${workflow.manifest.doi.tokenize(",").collect { doi -> " https://doi.org/${doi.trim().replace('https://doi.org/','')}"}.join("\n")}${workflow.manifest.doi ? "\n" : ""}
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x

Expand Down Expand Up @@ -113,7 +113,7 @@ workflow PIPELINE_INITIALISATION {
// Create channel from input file provided through params.input
//

Channel{% if nf_schema %}
channel{% if nf_schema %}
.fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json")){% else %}
.fromPath(params.input)
.splitCsv(header: true, strip: true)
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2 changes: 1 addition & 1 deletion nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
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18 changes: 9 additions & 9 deletions nf_core/pipeline-template/workflows/pipeline.nf
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Expand Up @@ -32,9 +32,9 @@ workflow {{ short_name|upper }} {
{%- if modules %}
main:

ch_versions = Channel.empty()
ch_versions = channel.empty()
{%- if multiqc %}
ch_multiqc_files = Channel.empty(){% endif %}
ch_multiqc_files = channel.empty(){% endif %}

{%- if fastqc %}
//
Expand Down Expand Up @@ -80,20 +80,20 @@ workflow {{ short_name|upper }} {
//
// MODULE: MultiQC
//
ch_multiqc_config = Channel.fromPath(
ch_multiqc_config = channel.fromPath(
"$projectDir/assets/multiqc_config.yml", checkIfExists: true)
ch_multiqc_custom_config = params.multiqc_config ?
Channel.fromPath(params.multiqc_config, checkIfExists: true) :
Channel.empty()
channel.fromPath(params.multiqc_config, checkIfExists: true) :
channel.empty()
ch_multiqc_logo = params.multiqc_logo ?
Channel.fromPath(params.multiqc_logo, checkIfExists: true) :
Channel.empty()
channel.fromPath(params.multiqc_logo, checkIfExists: true) :
channel.empty()

{%- if nf_schema %}

summary_params = paramsSummaryMap(
workflow, parameters_schema: "nextflow_schema.json")
ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
ch_workflow_summary = channel.value(paramsSummaryMultiqc(summary_params))
ch_multiqc_files = ch_multiqc_files.mix(
ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
{%- endif %}
Expand All @@ -102,7 +102,7 @@ workflow {{ short_name|upper }} {
ch_multiqc_custom_methods_description = params.multiqc_methods_description ?
file(params.multiqc_methods_description, checkIfExists: true) :
file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
ch_methods_description = Channel.value(
ch_methods_description = channel.value(
methodsDescriptionText(ch_multiqc_custom_methods_description))
{%- endif %}

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